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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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SingleR Issue. #218

Closed sivaraja23 closed 2 years ago

sivaraja23 commented 2 years ago

Hello! I am annotating my clusters using SingleR by this following code: SeqSingleR <- SingleR(test = MergedData, ref = mouse.rnaseq, assay.type.test=1, labels = mouse.rnaseq$label.main) SeqSingleR

MergedData is a Seurat object. But when I run this code, I get this following error:

Error in rownames<-(*tmp*, value = tolower(rownames(ref_data))) : attempt to set 'rownames' on an object with no dimensions

dtm2451 commented 2 years ago

See https://github.com/LTLA/SingleR/issues/145#issuecomment-692311765 test cannot receive a Seurat object directly.

sivaraja23 commented 2 years ago

See #145 (comment) test cannot receive a Seurat object directly.

I just tried this method and for some reason it is giving me the same error. I am not too sure where I could have gone wrong

dtm2451 commented 2 years ago

Is mouse.rnaseq an SCE or a Seurat? If it's a Seurat, then you should use the same function for this ref as well.

sivaraja23 commented 2 years ago

mouse.rnaseq is neither I believe. Its a built-in reference database from the SingleR package, its just a list of references.